Unstructured non-repetitive polypeptides having lcst behavior

Abstract

Described herein are unstructured polypeptides lacking any discernible repeat motif. Also described herein are fusion proteins including at least one of the unstructured polypeptides and at least one binding polypeptide. Further described are methods for treating a disease in a subject in need thereof. The methods may include administering to the subject an effective amount of the fusion protein.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 16/335,734, filed Mar. 22, 2019, which is the U.S. national stage entry, under 35 U.S.C. § 371, of International Application Number PCT/US2017/052887, filed Sep. 22, 2017, which claims priority to U.S. Provisional Application No. 62/399,123, filed Sep. 23, 2016, the entire contents of each of which are hereby incorporated by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under grant GM061232, awarded by the National Institutes of Health. The government has certain rights in the invention.

SEQUENCE LISTING

This instant application includes a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy created on Sep. 21, 2017, is named “028193-9228-WO01_As_Filed_Sequence_Listing.txt” and is 39986 bytes in size.

BACKGROUND

Proteins can be useful therapeutic agents when engineered for specificity, and selectivity for a clinical target. Their complexity, versatility, tolerability, and diversity often make them superior alternatives to small molecule drugs, and the long half-life, specificity, and selectivity can make them attractive for therapies. Although protein engineering allows for the development of potent therapeutics targeted toward a protein or receptor of interest, the body has many mechanisms with which to clear such protein therapies. Accordingly, there exists a need for reliable and broadly applicable protein delivery solutions.

SUMMARY

In one aspect, disclosed are unstructured polypeptides having no discernible repeat motif, wherein the polypeptide is soluble below the lower critical solution temperature (LCST), soluble above the upper critical solution temperature (UCST), or a combination thereof, wherein the LCST and UCST are each independently from about 0° C. to about 100° C.

In another aspect, disclosed are fusion proteins comprising at least one binding polypeptide and at least one of the disclosed unstructured polypeptides.

In another aspect, disclosed are methods for treating a disease in a subject in need thereof, the methods comprising administering to the subject an effective amount of a disclosed fusion protein.

In another aspect, disclosed are methods of diagnosing a disease in a subject, the methods comprising contacting a sample from the subject with a disclosed fusion protein; and detecting binding of the fusion protein to a target to determine presence of the target in the sample, wherein the presence of the target in the sample indicates the disease in the subject.

In another aspect, disclosed are methods of determining the presence of a target in a sample, the methods comprising contacting the sample with a disclosed fusion protein under conditions to allow a complex to form between the fusion protein and the target in the sample; and detecting the presence of the complex, wherein presence of the complex is indicative of the target in the sample.

In another aspect, disclosed are methods of determining the effectiveness of a treatment for a disease in a subject in need thereof, the methods comprising contacting a sample from the subject with a disclosed fusion protein under conditions to allow a complex to form between the fusion protein and a target in the sample; determining the level of the complex in the sample, wherein the level of the complex is indicative of the level of the target in the sample; and comparing the level of the target in the sample to a control level of the target, wherein if the level of the target is different from the control level, then the treatment is determined to be effective or ineffective in treating the disease.

In another aspect, disclosed are methods of diagnosing a disease in a subject, the methods comprising contacting a sample from the subject with a disclosed fusion protein; determining the level of a target in the sample; and comparing the level of the target in the sample to a control level of the target, wherein a level of the target different from the control level indicates disease in the subject.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram showing the amino acid compositions of the A[0.5] and A[0.2] sequences (SEQ ID NO: 1 and SEQ ID NO: 2). Correspondingly, the diagram also shows the amino acid compositions of polypeptides of SEQ ID NOs: 4, 6, 8, and 10 and SEQ ID NOs: 3, 5, 7, and 9, respectively.

FIG. 2 is a diagram showing the amino acid compositions of exemplary non-repetitive unstructured polypeptides (SEQ ID NOs: 11-18). Each non-repetitive unstructured polypeptide comprises 240 amino acids. Each amino acid sequence comprises approximately ⅙ proline (P) residues, approximately ⅓ glycine (G) residues, and approximately ½ X residues, where X is one or more amino acids selected from the group consisting of valine (V), alanine (A), leucine (L), lysine (K), threonine (T), isoleucine (I), tyrosine (Y), serine (S), and phenylalanine (F). Each of the selected amino acids for X can occur at equal frequencies to each other (SEQ ID NOs: 11-18).

FIG. 3(A)-(B) are graphs showing the characterization of the transition temperatures of the repetitive (SEQ ID NOs: 3-6) and exemplary non-repetitive polypeptides (SEQ ID NOs: 7-10). FIG. 3(A) is a graph showing repetitive and exemplary non-repetitive polypeptides comprising 200 amino acids. FIG. 3(B) is a graph showing repetitive and exemplary non-repetitive polypeptides comprising 400 amino acids.

FIG. 4(A)-(B) are graphs showing transition temperature characterization of exemplary non-repetitive unstructured polypeptides (SEQ ID NOs: 11-18). FIG. 4(A) is a graph showing transition temperature characterization of exemplary non-repetitive unstructured polypeptides at 25 μM in PBS. FIG. 4(B) is a graph showing transition temperature characterization of exemplary non-repetitive unstructured polypeptides in PBS at various concentrations of urea.

DETAILED DESCRIPTION

Elastin-like polypeptides (ELPs) are repetitive polypeptides. “ELP” refers to a polypeptide comprising the pentapeptide repeat sequence (VPGXG)_n, wherein X is any amino acid except proline and n is an integer greater than or equal to 1 (SEQ ID NO: 23). ELPs have been examined and characterized as having lower critical solution temperature (LCST) behavior. ELPs may include, for example, repeating subsequences of GAGVPGVGVP (SEQ ID NO: 1) or GVGVPGVGVPGAGVPGVGVPGVGVP (SEQ ID NO: 2), herein referred to as A[0.5] and A[0.2] respectively (see McDaniel, J. R et al. (2013) Biomacromolecules, which is incorporated by reference herein in its entirety). For example, A[0.2] rep-200 (SEQ ID NO: 3, (GVGVPGVGVPGAGVPGVGVPGVGVP)₈) includes the A[0.2] subsequence repeated 8 times for a total of 200 amino acids. A[0.5] rep-200 (SEQ ID NO: 4, (GAGVPGVGVP)₂₀) includes the A[0.5] subsequence repeated 20 times for a total of 200 amino acids. A[0.2] rep-400 (SEQ ID NO: 5, (GVGVPGVGVPGAGVPGVGVPGVGVP)₁₅) includes the A[0.2] subsequence repeated 16 times for a total of 400 amino acids. A[0.5] rep-400 (SEQ ID NO: 6, (GAGVPGVGVP)₄₀) includes the A[0.5] subsequence repeated 40 times for a total of 400 amino acids. The amino acid compositions of these sequences are depicted in FIG. 1.

Disclosed herein are unstructured, non-repetitive polypeptides that lack the requisite pentapeptide sequence of ELPs, yet unexpectedly still have LCST behavior. Accordingly, the disclosed unstructured polypeptides lack secondary structure (according to CD) and are thermally responsive, all without having a discernable repetitive sequence within the polypeptide.

1. Definitions

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present invention. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.

The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. The singular forms “a,” “an” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other embodiments “comprising,” “consisting of” and “consisting essentially of,” the embodiments or elements presented herein, whether explicitly set forth or not.

Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a concentration range is stated as 1% to 50%, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in this specification. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this application.

The modifier “about” used in connection with a quantity is inclusive of the stated value and has the meaning dictated by the context (for example, it includes at least the degree of error associated with the measurement of the particular quantity). The modifier “about” should also be considered as disclosing the range defined by the absolute values of the two endpoints. For example, the expression “from about 2 to about 4” also discloses the range “from 2 to 4.” The term “about” may refer to plus or minus 10% of the indicated number. For example, “about 10%” may indicate a range of 9% to 11%, and “about 1” may mean from 0.9-1.1. Other meanings of “about” may be apparent from the context, such as rounding off, so, for example “about 1” may also mean from 0.5 to 1.4.

As used herein, the term “affinity” refers to the binding strength of a binding polypeptide to its target (i.e., binding partner).

As used herein, the term “agonist” refers to an entity that binds to a receptor and activates the receptor to produce a biological response. An “antagonist” blocks or inhibits the action or signaling of the agonist. An “inverse agonist” causes an action opposite to that of the agonist. The activities of agonists, antagonists, and inverse agonists may be determined in vitro, in situ, in vivo, or a combination thereof.

As used herein, the term “biomarker” refers to a naturally occurring biological molecule present in a subject at varying concentrations that is useful in identifying and/or classifying a disease or a condition. The biomarker can include genes, proteins, polynucleotides, nucleic acids, ribonucleic acids, polypeptides, or other biological molecules used as an indicator or marker for disease. In some embodiments, the biomarker comprises a disease marker. For example, the biomarker can be a gene that is upregulated or downregulated in a subject that has a disease. As another example, the biomarker can be a polypeptide whose level is increased or decreased in a subject that has a disease or risk of developing a disease. In some embodiments, the biomarker comprises a small molecule. In some embodiments, the biomarker comprises a polypeptide.

As used herein, the terms “control,” “reference level,” and “reference” are used interchangeably. The reference level may be a predetermined value or range, which is employed as a benchmark against which to assess the measured result. “Control group” as used herein refers to a group of control subjects. The predetermined level may be a cutoff value from a control group. The predetermined level may be an average from a control group. Cutoff values (or predetermined cutoff values) may be determined by Adaptive Index Model (AIM) methodology. Cutoff values (or predetermined cutoff values) may be determined by a receiver operating curve (ROC) analysis from biological samples of the patient group. ROC analysis, as generally known in the biological arts, is a determination of the ability of a test to discriminate one condition from another, e.g., to determine the performance of each marker in identifying a patient having CRC. A description of ROC analysis is provided in P. J. Heagerty et al. (Biometrics 2000, 56, 337-44), the disclosure of which is hereby incorporated by reference in its entirety. Alternatively, cutoff values may be determined by a quartile analysis of biological samples of a patient group. For example, a cutoff value may be determined by selecting a value that corresponds to any value in the 25th-75th percentile range, preferably a value that corresponds to the 25th percentile, the 50th percentile or the 75th percentile, and more preferably the 75th percentile. Such statistical analyses may be performed using any method known in the art and can be implemented through any number of commercially available software packages (e.g., from Analyse-it Software Ltd., Leeds, UK; StataCorp LP, College Station, TX; SAS Institute Inc., Cary, NC.). The healthy or normal levels or ranges for a target or for a protein activity may be defined in accordance with standard practice.

As used herein, the term “expression vector” indicates a plasmid, a virus or another medium, known in the art, into which a nucleic acid sequence for encoding a desired protein can be inserted or introduced.

As used herein, the term “host cell” is a cell that is susceptible to transformation, transfection, transduction, conjugation, and the like with a nucleic acid construct or expression vector. Host cells can be derived from plants, bacteria, yeast, fungi, insects, animals, etc. In some embodiments, the host cell includes Escherichia coli.

As used herein, the term “reporter,” “reporter group,” “label,” and “detectable label” are used interchangeably herein. The reporter is capable of generating a detectable signal. The label can produce a signal that is detectable by visual or instrumental means. A variety of reporter groups can be used, differing in the physical nature of signal transduction (e.g., fluorescence, electrochemical, nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR)) and in the chemical nature of the reporter group. Various reporters include signal-producing substances, such as chromagens, fluorescent compounds, chemiluminescent compounds, radioactive compounds, and the like. In some embodiments, the reporter comprises a radiolabel. Reporters may include moieties that produce light, e.g., acridinium compounds, and moieties that produce fluorescence, e.g., fluorescein. In some embodiments, the signal from the reporter is a fluorescent signal. The reporter may comprise a fluorophore. Examples of fluorophores include, but are not limited to, acrylodan (6-acryloyl-2-dimethylaminonaphthalene), badan (6-bromo-acetyl-2-dimethylamino-naphthalene), rhodamine, naphthalene, danzyl aziridine, 4-[N-[(2-iodoacetoxy)ethyl]-N-methylamino]-7-nitrobenz-2-oxa-1,3-diazole ester (IANBDE), 4-[N-[(2-iodoacetoxy)ethyl]-N-methylamino-7-nitrobenz-2-oxa-1,3-diazole (IANBDA), fluorescein, dipyrrometheneboron difluoride (BODIPY), 4-nitrobenzo[c][1,2,5]oxadiazole (NBD), Alexa fluorescent dyes, and derivatives thereof. Fluorescein derivatives may include, for example, 5-fluorescein, 6-carboxyfluorescein, 3′6-carboxyfluorescein, 5(6)-carboxyfluorescein, 6-hexachlorofluorescein, 6-tetrachlorofluorescein, fluorescein, and isothiocyanate.

As used herein, the term “sample” or “test sample” can mean any sample in which the presence and/or level of a target is to be detected or determined. Samples may include liquids, solutions, emulsions, or suspensions. Samples may include a medical sample. Samples may include any biological fluid or tissue, such as blood, whole blood, fractions of blood such as plasma and serum, muscle, interstitial fluid, sweat, saliva, urine, tears, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, gastric lavage, emesis, fecal matter, lung tissue, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, cancer cells, tumor cells, bile, digestive fluid, skin, or combinations thereof. In some embodiments, the sample comprises an aliquot. In other embodiments, the sample comprises a biological fluid. Samples can be obtained by any means known in the art. The sample can be used directly as obtained from a patient or can be pre-treated, such as by filtration, distillation, extraction, concentration, centrifugation, inactivation of interfering components, addition of reagents, and the like, to modify the character of the sample in some manner as discussed herein or otherwise as is known in the art.

As used herein, the term “subject” as used herein can mean a mammal that wants or is in need of the herein described fusion proteins. The subject may be a human or a non-human animal. The subject may be a mammal. The mammal may be a primate or a non-primate. The mammal can be a primate such as a human; a non-primate such as, for example, dog, cat, horse, cow, pig, mouse, rat, camel, llama, goat, rabbit, sheep, hamster, and guinea pig; or non-human primate such as, for example, monkey, chimpanzee, gorilla, orangutan, and gibbon. The subject may be of any age or stage of development, such as, for example, an adult, an adolescent, or an infant.

As used herein, the term “transition” or “phase transition” refers to the aggregation of thermally responsive polypeptides. Phase transition occurs sharply and reversibly at a specific temperature called the LCST or the inverse transition temperature T_t. Below the transition temperature (LCST or T_t), a thermally responsive polypeptide is highly soluble. Upon heating above the transition temperature, a thermally responsive polypeptide may hydrophobically collapse and aggregate, forming a separate, gel-like phase. Phase transition behavior may be used to form drug depots within a tissue of a subject for controlled and/or slow release of the polypeptide. “Inverse transition cycling” refers to a protein purification method for thermally responsive polypeptides. The protein purification method may involve the use of thermally responsive polypeptide's reversible phase transition behavior to cycle the solution through soluble and insoluble phases, thereby removing contaminants and eliminating the need for chromatography.

As used herein, the term “subsequence” refers to a sequence of contiguous amino acids that occurs within another sequence of contiguous amino acids. A subsequence includes at least two amino acids. In some embodiments, a subsequence is 2 to 50, 2 to 20, 2 to 15, or 2 to 10 sequential amino acids in length. In some embodiments, a subsequence includes 3, 4, 5, 6, 7, 8, 9, or 10 sequential amino acids.

As used herein, the term “substantially identical” can mean that a first and second amino acid sequence are at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% over a region of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or 1100 amino acids.

As used herein, the term “treatment” or “treating,” when referring to protection of a subject from a disease, means preventing, suppressing, repressing, ameliorating, or completely eliminating the disease. Preventing the disease involves administering a composition of the present invention to a subject prior to onset of the disease. Suppressing the disease involves administering a composition of the present disclosure to a subject after induction of the disease but before its clinical appearance. Repressing or ameliorating the disease involves administering a composition of the present disclosure to a subject after clinical appearance of the disease.

As used herein, the term “valency” refers to the potential binding units or binding sites. The term “multivalent” refers to multiple potential binding units. The terms “multimeric” and “multivalent” are used interchangeably herein.

As used herein, the term “variant” with respect to a polynucleotide means (i) a portion or fragment of a referenced nucleotide sequence; (ii) the complement of a referenced nucleotide sequence or portion thereof; (iii) a polynucleotide that is substantially identical to a referenced polynucleotide or the complement thereof; or (iv) a polynucleotide that hybridizes under stringent conditions to the referenced polynucleotide, complement thereof, or a sequences substantially identical thereto.

A “variant” can further be defined as a peptide or polypeptide that differs in amino acid sequence by the insertion, deletion, or conservative substitution of amino acids, but retain at least one biological activity. Representative examples of “biological activity” include the ability to be bound by a specific antibody or polypeptide or to promote an immune response. Variant can mean a substantially identical sequence. Variant can mean a functional fragment thereof. Variant can also mean multiple copies of a polypeptide. The multiple copies can be in tandem or separated by a linker. Variant can also mean a polypeptide with an amino acid sequence that is substantially identical to a referenced polypeptide with an amino acid sequence that retains at least one biological activity. A conservative substitution of an amino acid, i.e., replacing an amino acid with a different amino acid of similar properties (e.g., hydrophilicity, degree and distribution of charged regions) is recognized in the art as typically involving a minor change. These minor changes can be identified, in part, by considering the hydropathic index of amino acids. See Kyte et al., J. Mol. Biol. 1982, 157, 105-132. The hydropathic index of an amino acid is based on a consideration of its hydrophobicity and charge. It is known in the art that amino acids of similar hydropathic indexes can be substituted and still retain protein function. In one aspect, amino acids having hydropathic indices of 2 are substituted. The hydrophobicity of amino acids can also be used to reveal substitutions that would result in polypeptides retaining biological function. A consideration of the hydrophilicity of amino acids in the context of a polypeptide permits calculation of the greatest local average hydrophilicity of that polypeptide, a useful measure that has been reported to correlate well with antigenicity and immunogenicity, as discussed in U.S. Pat. No. 4,554,101, which is fully incorporated herein by reference. Substitution of amino acids having similar hydrophilicity values can result in polypeptides retaining biological activity, for example immunogenicity, as is understood in the art. Substitutions can be performed with amino acids having hydrophilicity values within ±2 of each other. Both the hydrophobicity index and the hydrophilicity value of amino acids are influenced by the particular side chain of that amino acid. Consistent with that observation, amino acid substitutions that are compatible with biological function are understood to depend on the relative similarity of the amino acids, and particularly the side chains of those amino acids, as revealed by the hydrophobicity, hydrophilicity, charge, size, and other properties.

A variant can be a polynucleotide sequence that is substantially identical over the full length of the full gene sequence or a fragment thereof. The polynucleotide sequence can be 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the full length of the gene sequence or a fragment thereof. A variant can be an amino acid sequence that is substantially identical over the full length of the amino acid sequence or fragment thereof. The amino acid sequence can be 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the full length of the amino acid sequence or a fragment thereof.

2. Unstructured Polypeptides

Disclosed herein are unstructured polypeptides. The unstructured polypeptide may comprise any suitable polypeptide lacking secondary structure as observed by CD, and which lacks any discernable repetitive sequences. In addition, the unstructured polypeptide may be soluble below its LCST and/or above its UCST at a given concentration, thereby conferring a phase transition characteristic to the polypeptide such that it may be referred to as a “thermally responsive polypeptide.” LCST is the temperature below which the polypeptide is miscible. UCST is the temperature above which the polypeptide is miscible. The LCST is a separate and distinct temperature relative to the UCST. In some embodiments, the unstructured polypeptide may have only UCST behavior. In some embodiments, the unstructured polypeptide may have only LCST behavior. In some embodiments, the unstructured polypeptide may have both UCST and LCST behavior. In such embodiments, the UCST is higher than the LCST. The unstructured polypeptide may have a LCST of about 0° C. to about 100° C., such as about 10° C. to about 50° C., or about 20° C. to about 42° C. The unstructured polypeptide may have a UCST of about 0° C. to about 100° C., such as about 10° C. to about 50° C., or about 20° C. to about 42° C. In some embodiments, the unstructured polypeptide may have a transition temperature(s) (LCST and/or UCST) between room temperature (about 25° C.) and body temperature (about 37° C.). The unstructured polypeptide may have its LCST and/or UCST below body temperature or above body temperature at the concentration at which the unstructured polypeptide is administered to a subject. Thermally responsive unstructured polypeptides can phase transition at varying temperatures and concentrations. Thermally responsive unstructured polypeptides may not affect the binding or potency of a second polypeptide to which it is conjugated. In addition, thermally responsive unstructured polypeptides may be tuned to any number of desired transition temperatures, molecular weights, and formats.

The unstructured polypeptide may include varying amounts and types of amino acids. For example, the unstructured polypeptide may include a sequence of at least 50 amino acids, wherein at least 10% of the amino acids are proline (P), and at least 20% of the amino acids are glycine (G). In some embodiments, the unstructured polypeptide may include a sequence wherein at least 40% of the amino acids are selected from the group consisting of valine (V), alanine (A), leucine (L), lysine (K), threonine (T), isoleucine (I), tyrosine (Y), serine (S), and phenylalanine (F). In some embodiments, the unstructured polypeptide may include a sequence that does not contain three contiguous identical amino acids, wherein any 5-10 amino acid subsequence does not occur more than once in the unstructured polypeptide, and wherein when the unstructured polypeptide comprises a subsequence starting and ending with proline (P), the subsequence further includes at least one glycine (G).

In some embodiments, the unstructured polypeptide may include a sequence of at least 50 amino acids, wherein at least 10% of the amino acids are proline (P); wherein at least 20% of the amino acids are glycine (G); wherein at least 40% of the amino acids are selected from the group consisting of valine (V), alanine (A), leucine (L), lysine (K), threonine (T), isoleucine (I), tyrosine (Y), serine (S), and phenylalanine (F); wherein the sequence does not contain three contiguous identical amino acids; wherein any 5-10 amino acid subsequence does not occur more than once in the unstructured polypeptide; and wherein when the unstructured polypeptide comprises a subsequence starting and ending with proline (P), the subsequence further comprising at least one glycine (G).

Shorter subsequences of any of the non-repetitive sequences identified by the computer algorithm (as discussed below in the Examples) can maintain thermo-responsive behavior. Unstructured polypeptides comprising subsequences as short as 50 amino acids can satisfy the requirements of the algorithm, with similar composition as the full length sequence being sufficiently non-repetitive, because they are constrained by the same aforementioned sequence rules. Previous work has shown that intrinsic disorder can be encoded by unstructured peptides of less than 50 amino acids in length (see Radivojac et al. (2007) Biophys J., which is incorporated by reference herein in its entirety). Furthermore, ELPs as short as 50 amino acids can exhibit thermo-responsive LCST behavior, with measured transition temperatures within the range of 0 to 100° C. (see Aladini et al. (2016) J Pept Sci., which is incorporated by reference herein in its entirety). Accordingly in some embodiments, the unstructured polypeptide may comprise a 50 amino acid subsequence of any of SEQ ID NO: 7-18.

As mentioned above, the unstructured polypeptide may lack any discernable repeat motif of amino acids. The repetitiveness of the unstructured polypeptides may be characterized by its linguistic complexity score. Linguistic complexity score is defined by the total number of unique subsequences in a given sequence divided by the total number of unique subsequences possible for the same alphabet and window length (see Troyanskaya et al. (2002) Bioinformatics, which is incorporated by reference herein in its entirety). Further detail of linguistic complexity score can be found in Example 1 below. The unstructured polypeptide may have a linguistic complexity score of greater than 15, greater than 16, greater than 17, greater than 18, greater than 19, or greater than 20.

In some embodiments, the unstructured polypeptide may comprise an amino acid sequence selected from the group consisting of SEQ ID Nos. 7-18.

3. Fusion Proteins

Also disclosed herein are fusion proteins that can include at least one of the unstructured polypeptides, as described above. The fusion protein may further include at least one binding polypeptide and at least one linker.

In some embodiments, the fusion protein may include more than one binding polypeptide. The fusion protein may include at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 binding polypeptides. The fusion protein may include less than 30, less than 25, or less than 20 binding polypeptides. The fusion protein may include 1 to 30, such as 1 to 20, or 1 to 10 binding polypeptides. In such embodiments, the binding polypeptides may be the same or different from one another. In some embodiments, the fusion protein may include more than one binding polypeptide positioned in tandem to one another. In some embodiments, the fusion protein may include 2 to 6 binding polypeptides. For example, the fusion protein may include two binding polypeptides, three binding polypeptides, four binding polypeptides, five binding polypeptides, or six binding polypeptides.

In some embodiments, the fusion protein may include more than one unstructured polypeptide. The fusion protein may include at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 unstructured polypeptides. The fusion protein may include less than 30, less than 25, or less than 20 unstructured polypeptides. The fusion protein may include 1 to 30, such as 1 to 20, or 1 to 10 unstructured polypeptides. In such embodiments, the unstructured polypeptides may be the same or different from one another. In some embodiments, the fusion protein may include more than one unstructured polypeptide positioned in tandem to one another.

In some embodiments, the fusion protein may be arranged as a modular linear polypeptide. For example, the modular linear polypeptide may be arranged in one of the following structures: [binding polypeptide]_m-[linker]_k-[unstructured polypeptide]; [unstructured polypeptide]-[linker]_k-[binding polypeptide]_m; [binding polypeptide]_m-[linker]_k-[unstructured polypeptide]-[binding polypeptide]_m-[linker]_k-[unstructured polypeptide]; or [unstructured polypeptide]-[binding polypeptide]_m-[linker]_k-[unstructured polypeptide]-[binding polypeptide]_m, in which k and m are each independently an integer greater than or equal to 1. In some embodiments, m may be an integer less than or equal to 20. In some embodiments, m may be an integer equal to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20. In some embodiments, k may be an integer less than or equal to 10. In some embodiments, k may be an integer equal to 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the at least one binding polypeptide may be positioned N-terminal to the at least one unstructured polypeptide. In some embodiments, the at least one binding polypeptide may be positioned C-terminal to the at least one unstructured polypeptide.

In some embodiments, a fusion protein comprising one or more thermally responsive polypeptides may have a transition temperature between room temperature (about 25° C.) and body temperature (about 37° C.). The thermally responsive, unstructured polypeptide may have its LCST or UCST below body temperature or above body temperature at the concentration at which the fusion protein is administered to a subject.

The fusion protein may be expressed recombinantly in a host cell according to methods known within the art. The fusion protein may be purified by any suitable means known within the art. For example, the fusion protein may be purified using chromatography, such as liquid chromatography, size exclusion chromatography, or affinity chromatography, or through ultracentrifugation techniques. In some embodiments, the fusion protein may be purified without chromatography. In some embodiments, the fusion protein may be purified using inverse transition cycling.

a. Binding Polypeptide

The binding polypeptide may comprise any polypeptide that is capable of binding at least one target. The binding polypeptide may bind at least one target. “Target” may be an entity capable of being bound by the binding polypeptide. Targets may include, for example, another polypeptide, a cell surface receptor, a carbohydrate, an antibody, a small molecule, or a combination thereof. The target may be a biomarker. The target may be activated through agonism or blocked through antagonism. The binding polypeptide may specifically bind the target. By binding a target, the binding polypeptide may act as a targeting moiety, an agonist, an antagonist, or a combination thereof.

The binding polypeptide may be a monomer that binds to a target. The monomer may bind one or more targets. The binding polypeptide may form an oligomer. The binding polypeptide may form an oligomer with the same or different binding polypeptides. The oligomer may bind to a target. The oligomer may bind one or more targets. One or more monomers within an oligomer may bind one or more targets. In some embodiments, the fusion protein may be multivalent. In some embodiments, the fusion protein may bind multiple targets. In some embodiments, the activity of the binding polypeptide alone may be the same as the activity of the binding protein when part of a fusion protein.

In some embodiments, the binding polypeptide may comprise one or more scaffold proteins. As used herein, “scaffold protein” refers to one or more polypeptide domains with relatively stable and defined three-dimensional structures. Scaffold proteins may further have the capacity for affinity engineering. In some embodiments, the scaffold protein may be engineered to bind a particular target. In embodiments where the binding polypeptide comprises more than 1 scaffold protein, the scaffold proteins may be the same or different.

In some embodiments, the binding polypeptide may comprise Protein A. Protein A is a 42 kD protein originally derived from Staphylococcus aureus. It can exhibit high binding affinity to the constant region (Fc) of immunoglobulin G antibodies. Protein A includes 5 linked domains that are all able to bind antibody Fc. Immobilized protein A can be used for the purification of a variety of antibodies (see, e.g., Hober et al. (2006) J. Chromatogr. B, which is incorporated by reference herein in its entirety).

b. Linker

As mentioned above, the fusion protein may further include at least one linker. In some embodiments, the fusion protein may include more than one linker. In such embodiments, the linkers may be the same or different from one another. The fusion protein may include at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, or at least 100 linkers. The fusion protein may include less than 500, less than 400, less than 300, or less than 200 linkers. The fusion protein may include 1 to 1000 linkers, such as 10 to 900, 10 to 800, or 5 to 500 linkers.

The linker may be positioned in between a binding polypeptide and an unstructured polypeptide, in between binding polypeptides, in between unstructured polypeptides, or a combination thereof. Multiple linkers may be positioned adjacent to one another. Multiple linkers may be positioned adjacent to one another and in between the binding polypeptide and the unstructured polypeptide.

The linker may be a polypeptide of any suitable amino acid sequence and length. The linker may act as a spacer peptide. The linker may occur between polypeptide domains. The linker may sufficiently separate the binding domains of the binding polypeptide while preserving the activity of the binding domains. In some embodiments, the linker may comprise charged amino acids. In some embodiments, the linker may be flexible. In some embodiments, the linker may comprise at least one glycine and at least one serine. In some embodiments, the linker may comprise an amino acid sequence consisting of (Gly₄Ser)₃ (SEQ ID NO: 21). In some embodiments, the linker may comprise at least one proline. In some embodiments, the linker may comprise an amino acid sequence consisting of SEQ ID NO:22.

c. Polynucleotides

Further disclosed are polynucleotides encoding the fusion proteins detailed herein. A vector may include the polynucleotide encoding the fusion proteins detailed herein. To obtain expression of a polypeptide, one typically subclones the polynucleotide encoding the polypeptide into an expression vector that contains a promoter to direct transcription, a transcription/translation terminator, and if for a nucleic acid encoding a protein, a ribosome binding site for translational initiation. An example of a vector is pet24. Suitable bacterial promoters are well known in the art. Further disclosed is a host cell transformed or transfected with an expression vector comprising a polynucleotide encoding a fusion protein as detailed herein. Bacterial expression systems for expressing the protein are available in, e.g., E. coli, Bacillus sp., and Salmonella (Paiva et al., Gene 1983, 22, 229-235; Mosbach et al., Nature 1983, 302, 543-545, which are both incorporated by reference herein in their entirety). Kits for such expression systems are commercially available. Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available. Retroviral expression systems may also be used.

4. Administration

The fusion proteins as detailed above can be formulated in accordance with standard techniques known to those skilled in the pharmaceutical art. Such compositions comprising a fusion protein can be administered in dosages and by techniques known to those skilled in the medical arts taking into consideration such factors as the age, sex, weight, and condition of the particular subject, and the route of administration.

The fusion protein can be administered prophylactically or therapeutically. In prophylactic administration, the fusion protein can be administered in an amount sufficient to induce a response. In therapeutic applications, the fusion proteins can be administered to a subject in need thereof in an amount sufficient to elicit a therapeutic effect. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition of the fusion protein regimen administered, the manner of administration, the stage and severity of the disease, the general state of health of the patient, and the judgment of the prescribing physician.

The fusion protein can be administered by methods known in the art as described in Donnelly et al. (Ann. Rev. Immunol. 1997, 15, 617-648); Felgner et al. (U.S. Pat. No. 5,580,859, issued Dec. 3, 1996); Felgner (U.S. Pat. No. 5,703,055, issued Dec. 30, 1997); and Carson et al. (U.S. Pat. No. 5,679,647, issued Oct. 21, 1997), the contents of all of which are incorporated herein by reference in their entirety. The fusion protein can be complexed to particles or beads that can be administered to an individual, for example, using a vaccine gun. One skilled in the art would know that the choice of a pharmaceutically acceptable carrier, including a physiologically acceptable compound, depends, for example, on the route of administration.

The fusion proteins can be delivered via a variety of routes. Typical delivery routes include parenteral administration, e.g., intradermal, intramuscular or subcutaneous delivery. Other routes include oral administration, intranasal, intravaginal, transdermal, intravenous, intraarterial, intratumoral, intraperitoneal, and epidermal routes. In some embodiments, the fusion protein can be administered intravenously, intraarterially, or intraperitoneally to the subject.

The fusion protein can be a liquid preparation such as a suspension, syrup, or elixir. The fusion protein can be incorporated into liposomes, microspheres, or other polymer matrices (such as by a method described in Felgner et al., U.S. Pat. No. 5,703,055; Gregoriadis, Liposome Technology, Vols. I to III (2nd ed. 1993), the contents of which are incorporated herein by reference in their entirety). Liposomes can consist of phospholipids or other lipids, and can be nontoxic, physiologically acceptable and metabolizable carriers that are relatively simple to make and administer.

The fusion protein may be used as a vaccine. The vaccine can be administered via electroporation, such as by a method described in U.S. Pat. No. 7,664,545, the contents of which are incorporated herein by reference in its entirety. The electroporation can be by a method and/or apparatus described in U.S. Pat. Nos. 6,302,874; 5,676,646; 6,241,701; 6,233,482; 6,216,034; 6,208,893; 6,192,270; 6,181,964; 6,150,148; 6,120,493; 6,096,020; 6,068,650; and 5,702,359, the contents of which are incorporated herein by reference in their entirety. The electroporation can be carried out via a minimally invasive device.

In some embodiments, the fusion protein can be administered in a controlled release formulation. In some embodiments, the fusion protein may comprise one or more thermally responsive polypeptides, the thermally responsive polypeptide having a transition temperature such that the fusion protein remains soluble prior to administration and such that the fusion protein transitions upon administration to a gel-like depot in the subject. In some embodiments, the fusion protein may comprise one or more thermally responsive polypeptides, the thermally responsive polypeptide having a transition temperature such that the fusion protein remains soluble at room temperature and such that the fusion protein transitions upon administration to a gel-like depot in the subject. For example, in some embodiments, the fusion protein may comprise one or more thermally responsive polypeptides, the thermally responsive polypeptide having a transition temperature between room temperature (about 25° C.) and body temperature (about 37° C.), whereby the fusion protein can be administered to form a depot. As used herein, “depot” refers to a gel-like composition comprising a fusion protein that releases the fusion protein over time. In some embodiments, the fusion protein can be injected subcutaneously or intratumorally to form a depot (coacervate). The depot may provide controlled and/or slow release of the fusion protein. The depot may provide slow release of the fusion protein into the circulation or the tumor, for example. In some embodiments, the fusion protein may be released from the depot over a period of at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 7 days, at least 1 week, at least 1.5 weeks, at least 2 weeks, at least 2.5 weeks, at least 3.5 weeks, at least 4 weeks, or at least 1 month.

5. Detection

As used herein, the term “detect” or “determine the presence of” refers to the qualitative measurement of undetectable, low, normal, or high concentrations of one or more fusion proteins, targets, or fusion proteins bound to target. Detection may include in vitro, ex vivo, or in vivo detection. Detection may include detecting the presence of one or more fusion proteins or targets versus the absence of the one or more fusion proteins or targets. Detection may also include quantification of the level of one or more fusion proteins or targets. The term “quantify” or “quantification” may be used interchangeably, and may refer to a process of determining the quantity or abundance of a substance (e.g., fusion protein or target), whether relative or absolute. Any suitable method of detection falls within the general scope of the present disclosure. In some embodiments, the fusion protein may comprise a reporter attached thereto for detection. In some embodiments, the fusion protein may be labeled with a reporter. In some embodiments, detection of fusion protein bound to target may be determined by methods including but not limited to, band intensity on a Western blot, flow cytometry, radiolabel imaging, cell binding assays, activity assays, surface plasmon resonance (SPR), immunoassay, or by various other methods known in the art.

In some embodiments, including those wherein the fusion protein is an antibody mimic for binding and/or detecting a target, any immunoassay may be utilized. The immunoassay may be an enzyme-linked immunoassay (ELISA), radioimmunoassay (RIA), a competitive inhibition assay, such as forward or reverse competitive inhibition assays, a fluorescence polarization assay, or a competitive binding assay, for example. The ELISA may be a sandwich ELISA. Specific immunological binding of the fusion protein to the target can be detected via direct labels, attached to the fusion protein or via indirect labels, such as alkaline phosphatase or horseradish peroxidase. The use of immobilized fusion proteins may be incorporated into the immunoassay. The fusion proteins may be immobilized onto a variety of supports, such as magnetic or chromatographic matrix particles, the surface of an assay plate (such as microtiter wells), pieces of a solid substrate material, and the like. An assay strip can be prepared by coating the fusion protein or plurality of fusion proteins in an array on a solid support. This strip can then be dipped into the test biological sample and then processed quickly through washes and detection steps to generate a measurable signal, such as a colored spot.

6. Methods

a. Methods of Treating a Disease

In another aspect, disclosed are methods of treating a disease in a subject in need thereof. The method may comprise administering to the subject an effective amount of the fusion protein as described herein. The disease may be selected from cancer, metabolic disease, autoimmune disease, cardiovascular disease, and orthopedic disorders. In some embodiments, the disease may be a disease associated with a target of the at least one binding polypeptide.

Metabolic disease may occur when abnormal chemical reactions in the body alter the normal metabolic process. Metabolic diseases may include, for example, insulin resistance, non-alcoholic fatty liver diseases, type 2 diabetes, insulin resistance diseases, cardiovascular diseases, arteriosclerosis, lipid-related metabolic disorders, hyperglycemia, hyperinsulinemia, hyperlipidemia, and glucose metabolic disorders.

Autoimmune diseases may arise from an abnormal immune response of the body against substances and tissues normally present in the body. Autoimmune diseases may include, but are not limited to, lupus, rheumatoid arthritis, multiple sclerosis, insulin dependent diabetes mellitis, myasthenia gravis, Grave's disease, autoimmune hemolytic anemia, autoimmune thrombocytopenia purpura, Goodpasture's syndrome, pemphigus vulgaris, acute rheumatic fever, post-streptococcal glomerulonephritis, polyarteritis nodosa, myocarditis, psoriasis, Celiac disease, Crohn's disease, ulcerative colitis, and fibromyalgia.

Cardiovascular disease is a class of diseases that involve the heart or blood vessels. Cardiovascular diseases may include, for example, coronary artery diseases (CAD) such as angina and myocardial infarction (heart attack), stroke, hypertensive heart disease, rheumatic heart disease, cardiomyopathy, heart arrhythmia, congenital heart disease, valvular heart disease, carditis, aortic aneurysms, peripheral artery disease, and venous thrombosis.

Orthopedic disorders or musculoskeletal disorders are injuries or pain in the body's joints, ligaments, muscles, nerves, tendons, and structures that support limbs, neck, and back. Orthopedic disorders may include degenerative diseases and inflammatory conditions that cause pain and impair normal activities. Orthopedic disorders may include, for example, carpal tunnel syndrome, epicondylitis, and tendinitis.

Cancers may include, but are not limited to, breast cancer, colorectal cancer, colon cancer, lung cancer, prostate cancer, testicular cancer, brain cancer, skin cancer, rectal cancer, gastric cancer, esophageal cancer, sarcomas, tracheal cancer, head and neck cancer, pancreatic cancer, liver cancer, ovarian cancer, lymphoid cancer, cervical cancer, vulvar cancer, melanoma, mesothelioma, renal cancer, bladder cancer, thyroid cancer, bone cancers, carcinomas, sarcomas, and soft tissue cancers. In some embodiments, the cancer may be colorectal cancer. In some embodiments, the cancer may be colorectal adenocarcinoma.

In some embodiments, the present disclosure provides a method for using scaffold proteins in developing antibody mimetics for oncological targets of interest. With the emergence of scaffold protein engineering come the possibilities for designing potent protein drugs that are unhindered by steric and architectural limitations. Although potent protein drugs can be useful for diagnostics or treatments, successful delivery to the target region can pose a great challenge.

b. Methods of Diagnosing a Disease

In another aspect, disclosed are methods of diagnosing a disease. The methods may include administering to the subject a fusion protein as described herein, and detecting binding of the fusion protein to a target to determine presence of the target in the subject. The presence of the target may indicate the disease in the subject. In some embodiments, the methods may include contacting a sample from the subject with a fusion protein as described herein, determining the level of a target in the sample, and comparing the level of the target in the sample to a control level of the target, wherein a level of the target different from the control level indicates disease in the subject. In some embodiments, the disease may be selected from cancer, metabolic disease, autoimmune disease, cardiovascular disease, and orthopedic disorders, as detailed above. In some embodiments, the target may comprise a disease marker or biomarker. In some embodiments, the fusion protein may act as an antibody mimic for binding and/or detecting a target.

c. Methods of Determining the Presence of a Target

In another aspect, disclosed are methods of determining the presence of a target in a sample. The methods may include contacting the sample with a fusion protein as described herein under conditions to allow a complex to form between the fusion protein and the target in the sample, and detecting the presence of the complex. Presence of the complex may be indicative of the target in the sample. In some embodiments, the fusion protein may be labeled with a reporter for detection.

In some embodiments, the sample may be obtained from a subject and the method may further include diagnosing, prognosticating, or assessing the efficacy of a treatment of the subject. When the method includes assessing the efficacy of a treatment of the subject, then the method may further include modifying the treatment of the subject as needed to improve efficacy.

d. Methods of Determining the Effectiveness of a Treatment

In another aspect, disclosed are methods of determining the effectiveness of a treatment for a disease in a subject in need thereof. The methods may include contacting a sample from the subject with a fusion protein as detailed herein under conditions to allow a complex to form between the fusion protein and a target in the sample, determining the level of the complex in the sample, wherein the level of the complex is indicative of the level of the target in the sample, and comparing the level of the target in the sample to a control level of the target, wherein if the level of the target is different from the control level, then the treatment is determined to be effective or ineffective in treating the disease.

Time points may include prior to onset of disease, prior to administration of a therapy, various time points during administration of a therapy, after a therapy has concluded, or a combination thereof. Upon administration of the fusion protein to the subject, the fusion protein may bind a target, wherein the presence of the target indicates the presence of the disease in the subject at the various time points. In some embodiments, the target may comprise a disease marker or biomarker. In some embodiments, the fusion protein may act as an antibody mimic for binding and/or detecting a target. Comparison of the binding of the fusion protein to the target at various time points may indicate whether the disease has progressed, whether the diseased has advanced, whether a therapy is working to treat or prevent the disease, or a combination thereof.

In some embodiments, the control level may correspond to the level in the subject at a time point before or during the period when the subject has begun treatment, and the sample is taken from the subject at a later time point. In some embodiments, the sample may be taken from the subject at a time point during the period when the subject is undergoing treatment, and the control level corresponds to a disease-free level or to the level at a time point before the period when the subject has begun treatment. In some embodiments, the method may further include modifying the treatment or administering a different treatment to the subject when the treatment is determined to be ineffective in treating the disease.

7. Examples

Example 1: Identification of Non-Repetitive Unstructured Polypeptides

Non-repetitive permutated versions of ELPs were produced and examined. A computer algorithm was used to identify sequences comprising 200 or 400 amino acids, each with the same amino acid composition as the ELP counterpart, but with permutated or re-arranged ordering of the amino acids. The generated sequences were sufficiently non-repetitive, as they were rejected if they contained at least one subsequence comprising 5 to 10 amino acids that (a) contained three contiguous identical amino acids, (b) occurred more than once within the sequence, or (c) contained at least 2 prolines (P) separated by zero or more amino acids that are not glycine (G). These constraints promoted well-distributed prolines (P) and glycines (G) which have together been identified as structure-breaking residues.

The algorithm was used to additionally identify a panel of 8 non-repetitive sequences, each comprising 240 amino acids with ⅙ being proline (P) and ⅓ being glycine (G). The remaining amino acids were various combinations of 9 different amino acids found in elastin. The amino acid compositions of these sequences are depicted in FIG. 2.

The repetitiveness of each of the unstructured polypeptide sequences was quantified by calculating linguistic complexity scores. Linguistic complexity is defined by the total number of unique subsequences in a given sequence divided by the total number of unique subsequences possible for the same alphabet and window. Scores were calculated using the protein analysis tool, CIDER (see Holehouse et al. (2015) Biophys J., which is incorporated by reference herein in its entirety). The window length was set equal to the total sequence length for each sequence. The final score is given as the product of the linguistic complexity score and total sequence length to account for sequence length. The resulting final scores for the repetitive polypeptide sequences in SEQ ID NOs: 3-6 and non-repetitive polypeptide sequences in SEQ ID NOs: 7-18 are reported in Table 1. All final scores for the non-repetitive polypeptide sequences were greater than 15.0.

TABLE 1

Characterization of the repetitiveness of repetitive (SEQ ID NOs:
3-6) and non-repetitive (SEQ ID NOs: 7-18) polypeptide sequences
          Product of length and
SEQ ID NO linguistic complexity score

3         7.9
4         7.9
5         8.0
6         8.0
7         28.7
8         35.6
9         32.8
10        42.8
11        50.6
12        51.6
13        50.6
14        83.3
15        85.3
16        88.3
17        86.3
18        147.8

Example 2: Expression of Non-Repetitive Unstructured Polypeptides

All nucleotide sequences, unless indicated, were back-translated from amino acid sequences using codon scrambling (see Tang, N. C. et al. (2016) Nature Mater., which is incorporated by reference herein in its entirety). A N-terminal leader sequence encoding for Met-Ser-Lys-Gly-Pro-Gly (SEQ ID NO: 19) and a C-terminal His-tag tail encoding for Gly-Trp-Pro (SEQ ID NO: 20) were incorporated into the genes, unless indicated. All genes were synthesized by commercial synthesis and cloned into modified pET-24a(+) plasmids (Gen9 Inc., MA, USA and Genscript Inc., NJ, USA). The resulting plasmids were transformed into BL21 competent E. coli cells.

Colonies were inoculated in 2-5 mL of Terrific Broth (TB) plus 50 μg/mL kanamycin and grown overnight at 37° C. and 250 r.p.m. One milliliter of the starter cultures was inoculated in 1 L of TB plus 50 μg/mL kanamycin and grown for 6-7 h at 37° C. and 250 r.p.m. Expression was induced by the addition of IPTG at a final concentration of 1 mM, and the cells were grown for an addition 24 h. The unstructured polypeptides were purified by inverse transition cycling (ITC) as previously described (see Christensen et al. (2009) Curr Protoc Protein Sci., which is incorporated by reference herein in its entirety).

Example 3: Characterization of Non-Repetitive Unstructured Polypeptides

To characterize the inverse transition temperature of unstructured polypeptides, the 350 nm optical densities of 25 μM peptide solutions were monitored with a Cary 300 ultraviolet-visible spectrophotometer (Agilent Technologies) as a function of solution temperature. The inverse transition temperature was also monitored with the SYPRO Orange dye, whose fluorescence increases with the increasing hydrophobicity of the environment. Temperature responsive polymers exhibit phase transition due to the hydrophobic effect in aqueous solutions. Therefore, a StepOnePlus™ Real-Time PCR instrument was used to monitor fluorescence as a function of solution temperature. Inverse transition temperature was defined as the temperature at the maximum of the turbidity or fluorescence gradient.

Turbidity profiles, consisting of heating and cooling curves between about 0° C. and about 100° C., for all constructs at 25 μM in PBS show that non-repetitive versions of A[0.2](SEQ ID NOs: 7 and 9) and A[0.5] (SEQ ID NOs: 8 and 10), retain LCST phase behavior with transition temperatures similar to their repetitive counterparts (SEQ ID NOs: 3 and 5 and SEQ ID NOs: 4 and 6). In addition, the unstructured polypeptides exhibited lower critical solution temperature (LCST) behaviors between 0° C. and 100° C. (see FIG. 3(A)-(B) and FIG. 4(A)-(B)).

SEQUENCES

Repeated subsequences
A[0.5]:
SEQ ID NO: 1
GAGVPGVGVP

A[0.2]:
SEQ ID NO: 2
GVGVPGVGVPGAGVPGVGVPGVGVP

Repetitive polypeptides of A[0.5] and A[0.2]
A[0.2] rep, 200 amino acids:
SEQ ID NO: 3
(GVGVPGVGVPGAGVPGVGVPGVGVP)8

A[0.5] rep, 200 amino acids:
SEQ ID NO: 4
(GAGVPGVGVP)20

A[0.2] rep, 400 amino acids:
SEQ ID NO: 5
(GVGVPGVGVPGAGVPGVGVPGVGVP)16

A[0.5] rep, 400 amino acids:
SEQ ID NO: 6
(GAGVPGVGVP)40

Non-repetitive polypeptides with permutations of A[0.5] and
A[0.2]
A[0.2] nonrep, 200 amino acids:
SEQ ID NO: 7
PGGGVPGGVPGAVPGVPGAVVPVVGGVPGVVGVPGGVVPVGVVVPGVPVGVPGVPVVGGGVP

AGGVVPGGGVPVGGGVVPGVGVVPGGVPVVVGGGVGVPGVVPGVPGVGVPVGGVPGGGVVV

PGGVGVPVVGVVPGAPGVPGVPGGVGGVPVGVGVPGGGAPGVVPGGAVPGGAPVGGVGGGV

PGVGGVPGAPGGVPGG

A[0.5] nonrep, 200 amino acids:
SEQ ID NO: 8
PGGVPGVPAGGGAGVPGVPGAPAGGGAPGVAPGGVVPGVPGVAPVVGGGAPGGVPGAVPGVP

GGVPGGVVVPGGGVGAPGGVAPVGGGVPVVGGVPVGGVAPGVPVGVPGVGVGVGVPVGGGV

GGVPGVVPAGVPGGGVAGVVPVGGVINVVGAPGGGVGVPGAPGAGGVPGGAPGAPGVVAPG

GVPVGVVVPGVVPGGG

A[0.2] nonrep, 400 amino acids:
SEQ ID NO: 9
PGGVPGVGGGVPGVPGAPGVVPGVVVPGGVVPVGGVPGVPVVGGGVPVGGGVGGVPGAPGG

GVPGAPVGGVPVGGVVPGVGVPGAGGGVPGGVGVVPVGGGAPGGVPGVVPGVPVGGVPAGV

VPGGVGVGGGVVPGVVGVPGGGVGGGVGVPGGAPGGGVVGGGVPGGGVVPVVGGVPGAVP

GVPGVVVPVGGGVVPVGVPGGVVVPGVPGGVVGVPVVGVPGVGVVPGVPGVPVGVGVVVPG

VVPVGVGVPGVPGGGVPGVGVPVGGAPGVPGVPGVAVPGVVPGGAPGVPVGVVPVGVVPGGG

VGVVPGGVPGGVPGVPAGVPVGVPVGGVGGVVPGGGAPGVGVGVPAGVPGGVPVGVGGVTG

GVVPGVPAGGGVPVGVPGVGGVPVGAPGVPGGVP

A[0.5] nonrep, 400 amino acids:
SEQ ID NO: 10
PAGAVPGGVPVAGGVPVGAGVVAPGAPVGGAPGVVGVPGGGVPGVPVVGVGVGVPVGGGVG

VVPAGGGAPGGVGVVVPGVVPGAPAGGVPGVAPGGVGGVPGVVPGGGVVPGVAPGVPGVPG

GVPVGVPVGAAPGGGVPAVGVPGVGGGVPVVGAGAPGGVPGVAVPGAPGGVPVGGVPGGGV

GGVVPGGVPGAPVGVVPGVGVVPGVRAGVGVPGAPGAPGGGVPGGGAPVGGAGGVPGGVPG

VPGAPGVGVPGVGVPVGVPGVPGVPVGGGAGVPGGVAPGVAVPGGVGVPVVGGVPGAVPGVP

GVGGAPGVPGGGVVGVGVPGGVVPGVPGAGAPGGGAPGAPVGVPGGAPGVVPGVGGVPGAG

GGVVGGGVVPVGGGVVPGAPGGAPVGGVVGGVP

Non-repetitive polypeptides:
Each amino acid sequence comprises ⅙ proline (P) residues,
⅓ glycine (G) residues, and ½ Xresidues, where X is one or
more amino acids selected from the group consisting of valine
(V), alanine (A), leucine (L), lysine (K), threonine (T),
isoleucine (I), tyrosine (Y), serine (S), and phenylalanine
(F). Each of the selected amino acids for X occurs at equal
frequencies to each other.
SEQ ID NO: 11
PVGVPGVGGAPVVVGGAPVGVGGAGGVVPGAPVGAVAGVGAPGGAVPAGGAPGVGAPGVVP

GAVPGVGVGGVGGGVVVVVVVGVGGVPAGAVPVGGVAPVGVPVGAGGGAPAGGVPVAVGV

PVVGGGVPGVGVVGVAPGAPGAGVGVVAGAGAAAVAPVGVAPGVPGVPGAVVGVPGGVAPA

VVVGAVPGVVGVVPVGAPVVAGGVAVAPVGGAVPGVPGGVPGGGAPGAPVVGVPVGVP

SEQ ID NO: 12
PVGSPGSVPGVVPVSGVVVGGGSVPGSSPVVGVPSGVPVGSPVVGGGVSPGVGVPGVVVGVP

VGGGVGVPGGGVVGGVPVVVGVSVPSGVSPGGGVVVPVGSVSSGVPVVSVVGVSVVPGSVPV

GSPSSGVPGVVPGSPGGVVGSSVPSGSGGVSVPVGVGGSGVPGVPGSGSVVPVGVSPVGGGSG

SGVGSGSPGGSVPGGSPGVVPVGSPGVGGVPGVVGGSGSPGVPGGVGVGVPG

SEQ ID NO: 13
PVGTPGTVPGGVVPVGVTPVGGGTGTPTTVTVVGGVVVPGVPGGGTPGVPVGTPVVGGVGVGT

GTPGGTVPGGTPGVVPGTPGGVVPGTTVPTGTGTTPVVGVPTVGGVTPGVGGVPVVVGTGVPG

VPVGGGVGVVOVVVPGTVPVGVPGVVGGTVPVGTPTTGVPGVVPTGVITGGVGVPGGGVVGG

VVPGVTVPVGTVTTGVPVVTVGVVVPVGTVGGVVVGGGTTPGGVPGTPGVGG

SEQ ID NO: 14
GAVVVPGGAVGVPAGAVGGVGGVLVPAVGAVPGGGVPAVGVPVAGVVPGGLPGGAGVGALG

AAAPGGVPVGAALPGVAGVAPGGGLPGLGAGAGLGLAGALVLPGLGGVPGVPGGGLLPGGVP

LLGLPGVPAGLPGVLPVGLLLPGAPGVPALGVPLGVPGVAPGLPGAGGLPGVGAPCGLLPVGG

APAALGGLGLPGGGALGLLAPGGALVPGVGGVAPVAAGALLPGGAPLGVPALLAL

SEQ ID NO: 15
SSGSSGSGFFSGGVPSGGGVVFVPSFFGFFPSGSGGVVPGVPGGGVGVPGFVGVPVGGFPVGV

PGVFVPSVVGVPGFFVFPGVPGGSSSPGSPFGVFGGGSSGGGFPFGSSPGVVVSPGFGFGVPF

GVPVGGSVFFFPFGGGFPGGFPSGSFGVPGGGFVVPFGVSPGSPGFVPSFGSPGGFGGFSPF

SSGVGSPGGVPGVGVVSPGFPGGSPFGFPGSPGGSFGGSPSVFGSGSPGSFP

SEQ ID NO: 16
AAGGTGFFTGGAPGGTPTAFGGFTPFTFAGGGAPGFFAFPGAPGTFPTFGAPGAAPFGTTPGT

FFGFPGGTPGTPGAATPGFFGAFGFPGAFATFGFPGGGAGAAPAGTPGAPTAAGATTPGAGGT

TGGAPTGGGFAPTFFGFFPTGTGGAAPGAPGGGTTTFPGATPFGFPGGTPGTFGAPGGGFFPG

AGFGGGAPGAPAAAGGGTPGTATPGTFPTGAGTFPGTFPFGGGFPGGFPT

SEQ ID NO: 17
TILPGIGLPGGLPLTIGGILPILLGTTIGGIPGGGIIPGIGGGIPILTILILPTGLPGTPLTT

GTPGITGLGTPLGIGLIGTGIPGGGTGIPTGIPGTTLPGIPTLGGGIPLIGTPGGIGTIGIPG

TGTIIGIPGGGLLLIPGITPLIGLPGGITGTPGGGTGTTPTGLPGILLPGGLPGIPTGTPGTG

TPIGGLLILLTLPGLPGLGLPGLIPLGTGLTGGIPTGGIPGGICHPGILIT

SEQ ID NO: 18
PGTYPGYGYVYPTTGGIPGGVVPGGGTKKLPGKGKGGAKAPGTVPVGAGGGKIVPIYGIAPGK

YGYPGGGIVPGITTPGLPTGKKPYGGVPVLYGKLPGAPGIPTAGAPGYIAPGVPGGLVKGGTG

IAPLGIVILVYIGVGGIKGGALPIGGLYPGAGITGYPVGGGAPAGGIALKPGITPGTAAPGLP

GKGGKYTYPGGAPGGTGGVPGNPGLALKLGIPTKGGGIGLPYIGLLPGKPGG

SEQ ID NO: 19
Met-Ser-Lys-Gly-Pro-Gly

SEQ ID NO: 20
Gly-Trp-Pro

SEQ ID NO: 21
(Gly4Ser)3

SEQ ID NO: 22
PQPQPKKPQPKPEPEPQPQG

SEQ ID NO: 23
(VPGXG)n, wherein X is any amino acid except proline and n is
an integer greater than or equal to 1

Claims

1. An unstructured polypeptide having a lower critical solution temperature (LCST), an upper critical solution temperature (UCST), or a combination thereof,

wherein the unstructured polypeptide lacks a serial pentapeptide repeat of an elastin-like polypeptide (ELP), wherein the ELP repeat has the sequence (VPGXG)_n, where n is an integer greater than 1 and X is any amino acid except proline,

wherein the unstructured polypeptide has a linguistic complexity score, and wherein the product of the linguistic complexity score and the amino acid sequence length of the unstructured polypeptide is greater than 15;

wherein the polypeptide comprises a sequence of at least 50 amino acids, wherein at least 10% of the amino acids are proline (P), and wherein at least 20% of the amino acids are glycine (G),

wherein the polypeptide phase transitions above the LCST, phase transitions below the UCST, or a combination thereof, and

wherein the LOST and the UCST are each independently from about 0° C. to about 100° C.

2. The unstructured polypeptide of claim 1, wherein the LCST and UCST are each independently from about 25° C. to about 37° C.

3. The unstructured polypeptide of claim 1, wherein the unstructured polypeptide comprises:

(a) a sequence wherein at least 40% of the amino acids are selected from the group consisting of valine (V), alanine (A), leucine (L), lysine (K), threonine (T), isoleucine (I), tyrosine (Y), serine (S), and phenylalanine (F);

(b) a 50 amino acid subsequence of any of SEQ ID NO: 7-18;

(c) a sequence that does not contain three contiguous identical amino acids,

4. A fusion protein comprising at least one binding polypeptide and at least one unstructured polypeptide of claim 1.

5. The fusion protein of claim 4, wherein the fusion protein comprises a plurality of unstructured polypeptides.

6. The fusion protein of claim 4, wherein the fusion protein comprises a plurality of binding polypeptides.

7. The fusion protein of claim 6, further comprising a linker positioned between at least two adjacent binding polypeptides.

8. The fusion protein of claim 5, further comprising a linker positioned between at least two adjacent unstructured polypeptides.

9. The fusion protein of claim 7, wherein the linker comprises:

(a) at least one glycine and at least one serine, preferably wherein the linker comprises an amino acid sequence consisting of SEQ ID NO: 21 ((Gly₄Ser)₃); or

(b) an amino acid sequence consisting of SEQ ID NO: 22 (PQPQPKPQPKPEPEPQPQG).

10. The fusion protein of claim 8, wherein the linker comprises:

(a) at least one glycine and at least one serine, preferably wherein the linker comprises an amino acid sequence consisting of SEQ ID NO: 21 ((Gly₄Ser)₃); or

(b) an amino acid sequence consisting of SEQ ID NO: 22 (PQPQPKPQPKPEPEPQPQG).

11. The fusion protein of claim 6, wherein the plurality of binding polypeptides forms an oligomer.

12. The fusion protein of claim 4, wherein the binding polypeptide binds a target, and wherein the fusion protein binds more than one target, and/or wherein the binding polypeptide comprises Protein A.

13. The fusion protein of claim 4, further comprising at least one linker positioned between the at least one binding polypeptide and the at least one unstructured polypeptide, preferably wherein the fusion protein comprises a plurality of linkers between the at least one binding polypeptide and the at least one unstructured polypeptide.

14. The fusion protein of claim 4, wherein the at least one binding polypeptide is positioned a) N-terminal to the at least one unstructured polypeptide or b) C-terminal to the at least one unstructured polypeptide.